Oligo Design
Max Trauernicht
2020-11-05
knitr document van Steensel lab
TF reporter oligo design
Introduction
In this document, an oligo library of TF reporters will be generated. These oligos contain TF binding sites of ~30 selected TFs, random inactive spacing between them, followed by minimal promoters, and a barcode in the transcription unit.
Data processing
Path, Libraries, Parameters and Useful Functions
Custom functions
Functions used thoughout this script.
Data import
Analysis
Motif filtering and characterization
Session Info
## [1] "Run time: 12.37792 secs"## [1] "/DATA/usr/m.trauernicht/projects/SuRE-TF/library_design/gen-2"## [1] "Thu Nov 5 10:45:01 2020"## R version 3.6.3 (2020-02-29)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.7 LTS
##
## Matrix products: default
## BLAS: /usr/lib/libblas/libblas.so.3.6.0
## LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats4 parallel grid stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] ggrepel_0.8.1 ggbeeswarm_0.6.0
## [3] vwr_0.3.0 latticeExtra_0.6-29
## [5] lattice_0.20-38 stringdist_0.9.5.5
## [7] data.table_1.12.8 RColorBrewer_1.1-2
## [9] ggseqlogo_0.1 tibble_3.0.1
## [11] pheatmap_1.0.12 heatmaply_1.0.0
## [13] viridis_0.5.1 viridisLite_0.3.0
## [15] plotly_4.9.2.1 tidyr_1.0.0
## [17] stringr_1.4.0 readr_1.3.1
## [19] dplyr_0.8.5 magrittr_1.5
## [21] phylotools_0.2.2 ape_5.4-1
## [23] DNABarcodes_1.14.0 Matrix_1.2-18
## [25] gtools_3.8.1 SimRAD_0.96
## [27] zlibbioc_1.30.0 ShortRead_1.42.0
## [29] GenomicAlignments_1.20.1 SummarizedExperiment_1.14.1
## [31] DelayedArray_0.10.0 matrixStats_0.55.0
## [33] Biobase_2.44.0 Rsamtools_2.0.3
## [35] GenomicRanges_1.36.1 GenomeInfoDb_1.20.0
## [37] BiocParallel_1.18.1 Biostrings_2.52.0
## [39] XVector_0.24.0 IRanges_2.18.3
## [41] S4Vectors_0.22.1 BiocGenerics_0.30.0
## [43] universalmotif_1.2.1 seqLogo_1.50.0
## [45] seqinr_3.6-1 ggplot2_3.3.0
##
## loaded via a namespace (and not attached):
## [1] colorspace_1.4-1 ggtree_1.16.6 hwriter_1.3.2
## [4] ellipsis_0.3.0 farver_2.0.1 codetools_0.2-16
## [7] knitr_1.30 ade4_1.7-13 jsonlite_1.7.1
## [10] cluster_2.1.0 png_0.1-7 shiny_1.4.0
## [13] BiocManager_1.30.10 compiler_3.6.3 httr_1.4.1
## [16] rvcheck_0.1.7 fastmap_1.0.1 assertthat_0.2.1
## [19] lazyeval_0.2.2 later_1.1.0.1 htmltools_0.5.0
## [22] tools_3.6.3 gtable_0.3.0 glue_1.4.2
## [25] GenomeInfoDbData_1.2.1 Rcpp_1.0.5 vctrs_0.2.4
## [28] gdata_2.18.0 nlme_3.1-143 crosstalk_1.0.0
## [31] iterators_1.0.12 gbRd_0.4-11 xfun_0.19
## [34] ps_1.3.0 mime_0.9 lifecycle_0.2.0
## [37] dendextend_1.13.2 MASS_7.3-51.5 scales_1.1.0
## [40] TSP_1.1-7 promises_1.1.1 hms_0.5.3
## [43] yaml_2.2.1 gridExtra_2.3 stringi_1.5.3
## [46] gclus_1.3.2 foreach_1.4.7 tidytree_0.3.1
## [49] seriation_1.2-8 caTools_1.17.1.4 bibtex_0.4.2.2
## [52] Rdpack_0.11-1 rlang_0.4.8 pkgconfig_2.0.3
## [55] bitops_1.0-6 BH_1.72.0-3 evaluate_0.14
## [58] purrr_0.3.3 labeling_0.3 treeio_1.8.2
## [61] htmlwidgets_1.5.2 processx_3.4.1 tidyselect_1.1.0
## [64] R6_2.5.0 gplots_3.0.3 pillar_1.4.3
## [67] withr_2.1.2 RCurl_1.95-4.12 crayon_1.3.4
## [70] KernSmooth_2.23-16 rmarkdown_2.5 jpeg_0.1-8.1
## [73] digest_0.6.27 webshot_0.5.2 xtable_1.8-4
## [76] httpuv_1.5.4 munsell_0.5.0 beeswarm_0.2.3
## [79] registry_0.5-1 vipor_0.4.5